Comments on the cladistic approach to the phylogeny of the “bryophytes” by Mishler and Churchill

Brittonia - Basic errors are seen in failure to recognize problems of large phyletic gaps, failure to include fossil evidence which might help bridge phyletic gaps, inconsistency on transferability...     

An investigation into the usefulness of a cladistic approach to the study of the origin of anatomically modern humans

Cladistic analyses for the study of hominid evolution become very common during the last two decades, but little attention has been given to the appropriateness of the approach to studies being undertaken. This paper discusses how cladistic analyses have been used in studies of late Middle and Upper Pleicostocene hominids without due consideration of the problems inherent within the approach. It is concluded that in studies of the origin of anatomicaly modern humans a strict cladistic approach is inappropriate because it takes too narrow a view (presence/absence) of morphology, and in doing so does not allow for morphological variation. A phenetic approach which is interested in overall morphological similarity based on many characters and attempts to sample the total morphological variability evident within a sample would seem a more appropriate approach in such studies.     

Genome duplication and the origin of angiosperms

Despite intensive research, little is known about the origin of the angiosperms and their rise to ecological dominance during the Early Cretaceous. Based on whole-genome analyses of Arabidopsis thaliana, there is compelling evidence that angiosperms underwent two whole-genome duplication events early during their evolutionary history. Recent studies have shown that these events were crucial for the creation of many important developmental and regulatory genes found in extant angiosperm genomes. Here, we argue that these ancient polyploidy events might have also had an important role in the origin and diversification of the angiosperms.     

The origin and diversification of angiosperms

The angiosperms, one of five groups of extant seed plants, are the largest group of land plants. Despite their relatively recent origin, this clade is extremely diverse morphologically and ecologically. However, angiosperms are clearly united by several synapomorphies. During the past 10 years, higher-level relationships of the angiosperms have been resolved. For example, most analyses are consistent in identifying Amborella, Nymphaeaceae, and Austrobaileyales as the basalmost branches of the angiosperm tree. Other basal lineages include Chloranthaceae, magnoliids, and monocots. Approximately three quarters of all angiosperm species belong to the eudicot clade, which is strongly supported by molecular data but united morphologically by a single synapomorphy-triaperturate pollen. Major clades of eudicots include Ranunculales, which are sister to all other eudicots, and a clade of core eudicots, the largest members of which are Saxifragales, Caryophyllales, rosids, and asterids. Despite rapid progress in resolving angiosperm relationships, several significant problems remain: (1) relationships among the monocots, Chloranthaceae, magnoliids, and eudicots, (2) branching order among basal eudicots, (3) relationships among the major clades of core eudicots, (4) relationships within rosids, (5) relationships of the many lineages of parasitic plants, and (6) integration of fossils with extant taxa into a comprehensive tree of angiosperm phylogeny.     

A cladistic phylogeny of the family Patellidae (Mollusca: Gastropoda)

A phylogenetic hypothesis for the patellid limpets is reconstructed by cladistic analysis of morphological characters from 37 species, representing all but one of the living members of the family. Characters included in the analysis are derived from shell shape and microstructure, headfoot and pallial complex, radula and sperm. The species fall into four clades, providing the basis for a new phylogenetic classification into four monophyletic genera: Helcion (four species; southern Africa), Cymbula (eight species; southern Africa, eastern Atlantic, southern Indian Ocean), Scutellastra (17 species; southern and southwestern Africa, Australia, Indo-West Pacific, Eastern Pacific) and Patella (nine species; northeastern Atlantic and Mediterranean). The analysis suggests sister-group relationships between Helcion and Cymbula, and between Scutellastra and Patella. In combination with present-day patterns of geographical distribution, this phylogenetic hypothesis is used to discuss the historical biogeography of the Patellidae. Scutellastra may have originated in southern Africa and dispersed across the Pacific, or alternatively may be a primitively Tethyan group. Both Helcion and Cymbula appear to have originated in southern Africa, but three Cymbula species have dispersed respectively to northwest Africa, St Helena and the southern Indian Ocean. The patellids of the northeastern Atlantic form a single clade, Patella (including P. pellucida), which may have arrived by northward dispersal of an ancestor from southern Africa, or possibly by vicariance of a widespread ancestral Tethyan distribution. The known fossil record of patellids is too fragmentary to permit choice between these alternatives.     

The phylogeny of gutierrezia: An eclectic approach

One approach to the problem of deducing the genealogy of a set of organisms is to propose several hypotheses using different procedures, based on different evolutionary inferences. Such an approach was followed here, and four different phylogenies were constructed, three of them computer built. Consistency with independently obtained phenetic, cytological, and phytogeographical data was used to select the most probable phylogenetic tree among the four. It is shown that the most probable tree is one constructed under the assumption that character states found close to the mean and/or modal values for the genus are primitive. It is also shown that certain phylogenetic conclusions obtain in all four phylogenies.     

The tracheid-vessel element transition in angiosperms involves multiple independent features: cladistic consequences

Current definitions of tracheids and vessel elements are overly simple. These definitions are based on light microscope studies and have not incorporated information gained with scanning electron microscopy (SEM) or transmission electron microscopy (TEM). Current definitions are based primarily on angiosperms, especially eudicots, and were devised before many basal angiosperms were carefully studied. When all sources of information are taken into account, one can recognize changes in six characters in the evolution of tracheids into vessel elements in angiosperms (or vice versa) as well as in other groups of vascular plants. There is an appreciable number of taxa in which all criteria for vessel origin are not met, and thus incipient vessels are present. At the very least, vessel presence or absence should not be treated as a single binary character state change in construction of cladistic matrices. Increase in conductive area of an end wall by means of lysis of progressively greater areas of pit membrane and increase in pit area on the end wall (as compared to pit area on equivalent portions of lateral walls) are considered the most important usable criteria for recognizing intermediacy between tracheids and vessel elements. Primitive character states in vessel elements are briefly discussed to differentiate them from changes in character states that can be regarded as intermediate between tracheids and vessel elements.     

The origin of angiosperms: New and old problems

Recent palaeobotanical discoveries assisted by the thorough morphological analysis of 'living fossils'-archaic extant plants-have brought to light many unexpected features of the early angiosperms and their immediate precursors, while studies in palaeoecology have provided a basis for deciphering the chronology of evolutionary events and their environmental forcing. Our previous ideas of what is primitive and what angiosperm ancestors looked like are presently under revision. We now have a clearer picture of how macroevolution proceeds and how a large taxon could come into being.     

Seed plant phylogeny: gnetophytes are derived conifers and a sister group to Pinaceae

The phylogenetic position of gnetophytes has long been controversial. We sequenced parts of the genes coding for the largest subunit of nuclear RNA polymerase I, II, and III and combined these sequences with those of four chloroplast genes, two mitochondrial genes, and 18S rRNA genes to address this issue. Both maximum likelihood and maximum parsimony analyses of the sites not affected by high substitution levels strongly support a phylogeny where gymnosperms and angiosperms are monophyletic, where cycads are at the base of gymnosperm tree and are followed by ginkgos, and where gnetophytes are grouped within conifers as the sister group of pines. The evolution of several morphological and molecular characters of gnetophytes and conifers will therefore need to be reinterpreted.     

Air and the origin of the experimental plant physiology.

It is well known that oxygen and carbon dioxide are two chemicals which enter the plant metabolism as nutrients. The bases of this nowadays obvious statement were placed in the 18th century by means of the works of ingenious naturalists such as Robert Boyle, Stephen Hales, Joseph Priestley, Jam Ingenhousz, Lazzaro Spallanzani and Theodore De Saussure. Till the end of the 17th century, the atmospheric air was considered as an ineffable spirit, the function of which was of physical nature. Boyle was the first naturalist to admit the possibility that respiration were an exchange of vapours occurring in the blood. Stephen Hales realised that air could be fixed by plants under the influence of solar light. Priestley showed that plants could regenerate the bad air making it breathable. Ingenhousz demonstrated that the green parts of plants performed the complete purification of air only under the influence of the light. Spallanzani discovered that plants respire and guessed that the good air (oxygen) originated from the fixed air (carbon dioxide). Finally, Theodore De Saussure showed that plants were able to adsorb carbon dioxide and to release oxygen in a proportional air. All these discoveries benefited of the results coming from investigations of scholars of the so-called "pneumatic chemistry" (Boyle himself, George Ernst Stahl, Joseph Black, Priestley himself, and many more others. But among all the eminent scientists above mentioned stands out the genius of Antoine Laurent Lavoisier, who revolutionised the chemistry of the 18th century ferrying it towards the modern chemistry.     

Integrating Early Cretaceous fossils into the phylogeny of living angiosperms:Magnoliidae and eudicots

Over the past 25 years, discoveries of Early Cretaceous fossil flowers, often associated with pollen and sometimes with vegetative parts, have revolutionized our understanding of the morphology and diversity of early angiosperms. However, few of these fossils have been integrated into the increasingly robust phylogeny of living angiosperms based primarily on molecular data. To remedy this situation, we have used a morphological dataset for living basal angiosperms (including basal eudicots and monocots) to assess the most parsimonious positions of early angiosperm fossils on cladograms of Recent plants, using constraint trees that represent the current range of hypotheses on higher-level relationships, and concentrating on Magnoliidae (the clade including Magnoliales, Laurales, Canellales, and Piperales) and eudicots. In magnoliids, our results confirm proposed relationships of Archaeanthus (latest Albian?) to Magnoliaceae, Endressinia (late Aptian) to Magnoliales (the clade comprising Degeneria, Galbulimima, Eupomatia, and Annonaceae), and Walkeripollis pollen tetrads (late Barremian?) to Win-teraceae, but they indicate that Mauldinia (early Cenomanian) was sister to both Lauraceae and Hernandiaceae rather than to Lauraceae alone. Among middle Albian to early Cenomanian eudicots, we confirm relationships of Nelumbites to Nelumbo, platanoid inflorescences and Sapindopsis to Platanaceae, and Spanomera to Buxaceae. With the possible exception of Archaeanthus, these fossils are apparently not crown group members of living families but rather stem relatives of one or more families.     

The use of cladistic principles in the phylogeny and biogeography of the Lacerta

The methodology used in Phylogenetics remains one of the more interesting problems in comparative biology. Among the methods used, the cladistic is the most accurate. In the present case, among the Saurians, the characters chosen appeared early and cannot be referred to any adaptation bound to an evolutive progress. We have successively considered their distribution in the classification, their polarity and one phylogenetic hypothesis based on the Hennig's concepts. Such a work leads necessarily to systematical conclusions. For instance, we note the heterogeneity of some families. Among the Iguania, the Iguanidea are polyphyletics, the north-american forms breaking up from the other very early. Among the Scincomorpha, the Lacertilia result from two parts of different origins. This research verifies some systematic cuttings in the modern classification: among the Anguimorpha, the separation between Helodermatidea and the group, Varanidea-Lanthanotidea. The characters studied show a non-random distribution in the classification and show also some consistency with the geographical distribution of the extant Saurians. Therefore, it is important to search for the most parsimonious geographical hypothesis, which is in concern with the present data on the continental drift and generally on the history of the Earth, and which strengthens the cladograms posed from the selected characters.     

Optimization theory in plant evolution: An overview of long-term evolutionary prospects in the angiosperms

Examination of literature shows that a number of authors regard outbreeding and heterozygosity as the prevalent factors associated with long-term successful evolution in the angiosperms. A number of plant evolutionists, however, have doubted the truth of such an assumption. Everincreasing reports of the existence of arboreal angiospermous apomixis in tropical forests of the Neotropics and the Far East undermined a thinking which, recently, has rested on optimality. Finding apomixis in trees surprised authors, who held biased opinions about the determinism of outbreeding as the major guiding factor in the evolutionary history of the angiosperms. The thinking that apomixis may turn out to be a regular mating system of the flowering plants met with the approval of some authors, who wondered about the true penetration of the phenomenon among the higher plants. The fact that one-third of all known flowering plants are autogamous has cast further doubt on the deterministic infallibility of outbreeding and successful long-term evolution. Despite claims that the breeding system is directly involved with fitness, while determining the course of optimized evolution, there is comparatively little hard evidence to substantiate a hypothesis which, in the last analysis, has rested principally on common sense. Rather, if continuing field research happens to unveil new cases of woody angiospermous apomixis, a prediction is advanced that the next two biomes to show regular incidence of the phenomenon are Africa’s paleotropical savannas and humid forests. If evolution is partly or wholly dependent on the breeding system to proceed, current knowledge supports views that further enhancement of organic diversification vis-à-vis selection and adaptednesss rests on three major tested mating systems: outbreeding, inbreeding and apomixis.     

Phylogenetic evidence for the herbaceous origin of angiosperms

The ancestral angiosperm is commonly interpreted as an arborescent to shrubby magnolialean with large, multiparted, complex flowers. We examined this hypothesis using a phylogenetic analysis of new and reevaluated characters polarizabled with outgroup comparison. Our cladistic analysis of basal angiosperms placed the nonmagnolialeanChloranthaceae andPiperaceae at the bottom of the tree. We further inferred the probable ancestral states of characters not polarizable with outgroup comparison by examining their distribution among taxa at the base of our cladogram. The sum of ancestral character states suggests that the protoangiosperm was a diminutive, rhizomatous to scrambling perennial herb, with small, simple flowers.     

The phylogeny of land plants: A cladistic analysis based on male gametogenesis

A cladistic analysis was carried out to resolve phylogenetic pattern among bryophytes and other land plants. The analysis used 22 taxa of land plants and 90 characters relating to male gametogenesis.Coleochaete orChara/Nitella were the outgroups in various analyses using HENNIG86, PAUP, and MacClade, and the land plant phylogeny was unchanged regardless of outgroup utilized. The most parsimonious cladograms from HENNIG86 (7 trees) have treelengths of 243 (C.I. = 0.58, R.I. = 0.82). Bryophytes are monophyletic as are hornworts, liverworts, and mosses, with hornworts identified as the sister group of a liverwort/moss assemblage. In vascular plants, lycophytes are polyphyletic andSelaginella is close to the bryophytes.Lycopodium is the sister group of the remaining vascular plants (minusSelaginella). Longer treelengths (over 250) are required to produce tree topologies in which either lycophytes are monophyletic or to reconstruct the paraphyletic bryophyte phylogeny of recent authors. This analysis challenges existing concepts of bryophyte phylogeny based on more classical data and interpretations, and provides new insight into land plant evolution.